An atomic force microscope (AFM) may measure atomic scales by scanning a surface of a substrate using a probe. The probe may scan the surface of the substrate by using a contact method, a non-contact method, or an intermittent contact method. The AFM may provide an image of a change in position of the probe ascending and descending. Additionally, the AFM may be applied to measure a friction force, a magnetic property, an electric property, an electrochemical property, and electric capacity of the surface of the substrate. Generally, the probe of the ATM may be easily worn or damaged. Interaction between the surface of the substrate and the AFM may be observed by using an electron microscope. A state of the probe of the AFM may be in-situ monitored by using the electron microscope.